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| Status |
Public on Jun 07, 2019 |
| Title |
Biosample_8606_4132_58667_HYL2CBGX2_K562_InSituHiC_HS_2_GCCAAT |
| Sample type |
SRA |
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| Source name |
K562 immortalized cell line
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| Organism |
Homo sapiens |
| Characteristics |
cell line: K562
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| Treatment protocol |
Growing K562 cells were concentrated in 10 ml of the same growth medium and placed in a 37°C water bath (NHS) or 42°C water bath (HS) for 30 min.
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| Growth protocol |
Human K562 chronic myelogenous leukemia cells were maintained at 37°C in a humidified 5% CO2 atmosphere and cultured in RPMI medium containing 10% FBS, 100 U/ml penicillin & 100 μg/ml streptomycin.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were crosslinked with 1% formaldehyde for 10 min, quenched and permeabilized. Nuclei were digested with MboI and ends were biotinylated with biotin-14-dATP followed by in-situ ligation. Crosslinks were reversed and DNA was purified, sonicated and pulled down by streptavidin beads.
DNA was end repaired with T4 DNA polymerase, DNA polymerase I large (Klenow) polymerase and T4 polynucleotide kinase. DNA ends were adenylated by dATP and Klenow (3'-5' exo-) polymerase. Illumina Truseq adapters were ligated to the DNA ends and PCR amplified for 10 cycles. Library was purified with Qiaquick PCR purfication kit and sequenced on Illumina Nextseq 500.
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Fastq files were processed using the Aiden Lab's Juicer pipeline. The reference genome used was hg19, and the restriction enzyme was MboI
The resulting contact matices (.hic files) were produced at resolutions of 20 Mb, 10 Mb, 5 Mb, 2.5 Mb, 1 Mb, 500 Kb, 250 Kb, 100 Kb, 50 Kb, 25 Kb, 10 Kb, 5 Kb, and 1 Kb, using only high quality reads (MAPQ score >= 30)
Genome_build: hg19
Supplementary_files_format_and_content: hic files - highly compressed binary files that store contact matrices at multiple resolutions
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| Submission date |
May 06, 2019 |
| Last update date |
Jun 09, 2019 |
| Contact name |
Charles Danko |
| E-mail(s) |
dankoc@gmail.com
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| Organization name |
Cornell University
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| Department |
Computational Biology
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| Lab |
Danko Lab
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| Street address |
235 Hungerford Drive
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| City |
Ithaca |
| State/province |
NY |
| ZIP/Postal code |
14850 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (2) |
| GSE130758 |
Chromatin conformation remains stable upon extensive transcriptional changes driven by heat shock [K562] |
| GSE130778 |
Chromatin conformation remains stable upon extensive transcriptional changes driven by heat shock |
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| Relations |
| BioSample |
SAMN11582761 |
| SRA |
SRX5797625 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3753208_K562_HS_2_inter_30.hic |
2.3 Gb |
(ftp)(http) |
HIC |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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